Get advice on new alignment filter

[davidbenjamin]

We need a plan for this. It would be nice to use the SV team's in-memory BWA-mem binding, but it's not clear that tweaking settings would be enough to capture possible alignment errors in a BWA-aligned bam file. CGA has used Novo-align and BLAT in the past. We'll want to talk with Chris, Heng, and Julian about this.

[davidbenjamin]

Talked to Heng, who suggested which parameters to use with the BWA-mem binding to maximize sensitivity to multi-mapped reads.

[davidbenjamin]

Next: talk to Julian.

[davidbenjamin]

Done. Julian agrees that BWA is worth trying, and confirmed that CGA is using BLAT C++ bindings with out of the box settings.